User: Johannes Rainer

gravatar for Johannes Rainer
Reputation:
880
Status:
Trusted
Location:
Italy
Twitter:
@jotsetung
Last seen:
30 minutes ago
Joined:
2 years, 9 months ago
Email:
j**************@eurac.edu

PhD, Bioinformatics Group, Center for Biomedicine, EURAC Research, Bolzano, Italy

 

Posts by Johannes Rainer

<prev • 192 results • page 1 of 20 • next >
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Comment: C: Ensembl 90 has been released
... EnsDb databases for Ensembl 90 will follow soon - stay tuned.   cheers, jo ...
written 15 hours ago by Johannes Rainer880
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Comment: C: EnsemblDb: how to retrieve gene name / description?
... Dear Guido, thanks for your suggestion. I've opened an issue over at the github repo https://github.com/jotsetung/ensembldb/issues/53 and will think of a possible solution. ...
written 6 days ago by Johannes Rainer880
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Answer: A: EnsemblDb: how to retrieve gene name / description?
... Dear Guido, the naming of the columns in an EnsDb might be misleading, but they reflect the naming convention from Ensembl. Each gene there has a name which is stored in columns gene_name (or GENENAME) in the EnsDb. In addition there is the description field for each gene, but I didn't put them in ...
written 7 days ago by Johannes Rainer880
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Comment: C: errors with makeTxDbFromBiomart
... I've now pushed the fix (for Bioconductor release 3.5 and Bioconductor 3.6 development version) to Bioc svn. Means within the next few days an updated version of ensembldb (version 2.0.4) should be available that can generate the EnsDb also from the GTF. To update ensembldb: library(BiocInstaller) ...
written 18 days ago by Johannes Rainer880
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Answer: A: errors with makeTxDbFromBiomart
... Indeed, there was a bug in ensDbFromGtf that failed to parse the GTF header properly (the genome version contained a white space). I've fixed that and will push the fix to Bioconductor soon. In the meanwhile you can download the EnsDb package for your species using the link below https://www.dropb ...
written 21 days ago by Johannes Rainer880
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Comment: C: errors with makeTxDbFromBiomart
... I'll have a look into this. If everything else fails I'll create the EnsDb using the Ensembl perl API.   cheers, jo ...
written 22 days ago by Johannes Rainer880
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Comment: C: BoF "Writing papers in Rmarkdown, BiocStyle... (and books, posters)"
... Regarding tables for markdown (and other): I'm using the pander package (with the pandoc.table function), which supports also captions/titles. ...
written 27 days ago by Johannes Rainer880
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Answer: A: Is it possible to get Ensembl gene descriptions with ensembldb?
... OK, it's now available for Ensembl 87 (still working on the Ensembl 88) that you can get from AnnotationHub: > library(AnnotationHub) > ah <- AnnotationHub() > edb <- query(ah, "EnsDb.Hsapiens.v87") > edb EnsDb for Ensembl: |Backend: SQLite |Db type: EnsDb |Type of Gene ID: Ensem ...
written 9 weeks ago by Johannes Rainer880
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Comment: C: ensembldb salmon deseq2 txt2import right tool?
... I create EnsDbs for all species defined in Ensembl, this includes also Danio rerio. Once I'm done, these EnsDbs will show up in the AnnotationHub of the Bioc devel version. Note that the Danio rerio EnsDbs for Ensembl 87 and 88 are already in AnnotationHub ...
written 10 weeks ago by Johannes Rainer880
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Comment: C: BiocParallel: messages shown only when processes finished
... Thanks Martin for this explanation! ...
written 10 weeks ago by Johannes Rainer880

Latest awards to Johannes Rainer

Scholar 11 weeks ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Great Question 11 weeks ago, created a question with more than 5,000 views. For Problem with biomart's listMarts function
Student 3 months ago, asked a question with at least 3 up-votes. For Easy way to sort GRangesList by seqname/start position?
Student 4 months ago, asked a question with at least 3 up-votes. For Problem with biomart's listMarts function
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Problem running dexseq in parallel using BiocParallel
Scholar 4 months ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: makeTxDbFromBiomart Error: 1: Space required after the Public Identifier
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: biomaRt no longer works with proxy after upgrade
Scholar 16 months ago, created an answer that has been accepted. For A: Missing SYMBOL keytype in EnsDb.Hsapiens.v75
Scholar 16 months ago, created an answer that has been accepted. For A: ensembldb: ensDbFromGtf error with ensembl version 74
Scholar 16 months ago, created an answer that has been accepted. For A: biomaRt no longer works with proxy after upgrade
Scholar 16 months ago, created an answer that has been accepted. For A: biomaRt package problem
Scholar 16 months ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Popular Question 19 months ago, created a question with more than 1,000 views. For Problem with biomart's listMarts function
Appreciated 20 months ago, created a post with more than 5 votes. For A: biomaRt no longer works with proxy after upgrade
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: makeTxDbFromBiomart Error: 1: Space required after the Public Identifier
Centurion 20 months ago, created 100 posts.
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: biomaRt no longer works with proxy after upgrade
Scholar 21 months ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: biomaRt no longer works with proxy after upgrade
Scholar 21 months ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Supporter 21 months ago, voted at least 25 times.
Scholar 21 months ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Autobiographer 2.2 years ago, has more than 80 characters in the information field of the user's profile.

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